Hi Steve-
Unfortunately, your e-mail came about 10 minutes too late for me. I
did indeed destroy my old version (3.0) of R. I did use the
R-devel*.pkg available at att.com<http: att.com=""> but I must have
missed the installer prompt that prevented it from killing my current
release install.
Do you have any advice for how I can fix this? I tried to restore my
release version of R from a Time Machine backup but I still get the
message R cannot be opened because of a problem.
thanks,
Kristina
------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139
On Jan 17, 2014, at 5:05 PM, Steve Lianoglou
<lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote:
Hi,
Perhaps a more user-friendly way to run w/ both versions is to simply
install the R-devel *.pkg available from
http://r.research.att.com<http: r.research.att.com=""/>
specifically:
http://r.research.att.com/snowleopard/R-devel/R-devel-snowleopard-
signed.pkg
Make sure you pay close attention to the installer and follow the
instructions provided in the splash window so that the installation
doesn't blow out your current (release) install (this will involve
running some command from the terminal that has to do w/ the install
receipts, or something).
Then, to switch between R and R-devel, you "simply" use the RSwitch
app available from the same site:
http://r.research.att.com/RSwitch-1.2.dmg
Which is an app front end w/ simply does some swapping of symlinks so
that the right links point to the right version of R that you want to
run.
Note that I believe this approach isn't amenable to running both
versions of R *at the same time.*
-steve
[[alternative HTML version deleted]]

Hi Kristina,
On Fri, Jan 17, 2014 at 2:29 PM, Kristina M Fontanez <fontanez at="" mit.edu=""> wrote:
> Hi Steve-
>
> Unfortunately, your e-mail came about 10 minutes too late for me. I
did indeed destroy my old version (3.0) of R. I did use the
R-devel*.pkg available at att.com<http: att.com=""> but I must have
missed the installer prompt that prevented it from killing my current
release install.
>
> Do you have any advice for how I can fix this? I tried to restore my
release version of R from a Time Machine backup but I still get the
message ?R cannot be opened because of a problem?.
Ack -- so .. "[Un]suffered Consequences" ... sorry to hear that.
It's actually been a long time since this has happened to me, so I
forget the exact details of the collateral damage you've just suffered
:-)
The good news is that it's not too onerous to recover from scratch.
Just download the latest R-release installer pkg from CRAN. The
installer will (should) contain the same warning telling you what the
command is to perform a "non-destructive" isntall. For what it's
worth, you simply have to open up a terminal and type in the following
command:
sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg
Then continue with the installation and all will be Feng Shui.
After doing so, launching "R" from the terminal should now open
R-3.0.2 (no need to use RSwitch). Just do the usual biocinstall (ie.
source the biocLite script then re-install the packages you need).
Being at MIT, the bandwidth available to you should make this a quick
process, especially since the packages for the mac do not need to be
compiled for installation.
The good news is that after you've done that, you'll have a "working"
multi-R environment you can jump back and forth between by simply
using RSwitch.
HTH,
-steve
--
Steve Lianoglou
Computational Biologist
Genentech

Hi Steve-
Thanks for the help. I deleted the development and corrupted release
versions of R from my computer. Then, I downloaded the release
version. Next, I renamed the release version in my Applications folder
to R_3.0. Then I downloaded the installer package from
att.com<http: att.com=""> for the development version. I opened up a
terminal and in my / directory I typed in sudo pkgutil forget
org.r-project.R.x86_64.fw.pkg.
parsons-three-sixty:/ fontanez$ sudo pkgutil --forget
org.r-project.R.x86_64.fw.pkg
Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'.
Then, I proceeded to install the development version from the R
development installer package. It installed correctly and I was able
to download the development version of DESeq and my other packages.
However, this is where I ran into a problem.
I shut down R and opened up the R_3.0 app from my Applications. It
opened, which was good but it drops a ton of warnings. Anytime I try
to type something (as Im typing) that anyNA is not a builtin
function error pops up. It looks like my R 3.0 is still corrupted. I
didnt change anything in /Library/Frameworks - should I have done
that as well, like Dan suggested?
Thanks,
Kristina
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package methods was built under R version 3.1.0
2: package "methods" in options("defaultPackages") was not found
3: package datasets was built under R version 3.1.0
4: package datasets in options("defaultPackages") was not found
5: package utils was built under R version 3.1.0
6: package utils in options("defaultPackages") was not found
7: package grDevices was built under R version 3.1.0
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package grDevices in options("defaultPackages") was not found
2: package graphics was built under R version 3.1.0
Error : object 'anyNA' not found whilst loading namespace 'grDevices'
In addition: Warning messages:
1: package graphics in options("defaultPackages") was not found
2: package stats was built under R version 3.1.0
During startup - Warning messages:
1: package stats in options("defaultPackages") was not found
2: package methods was built under R version 3.1.0
3: package methods in options("defaultPackages") was not found
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
[History restored from /Users/fontanez/.Rapp.history]
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
> library(DESeq2)
Loading required package: GenomicRanges
Loading required package: methods
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
In addition: Warning messages:
1: package DESeq2 was built under R version 3.1.0
2: package GenomicRanges was built under R version 3.1.0
3: In get(".__S3MethodsTable__.", envir = env, inherits = FALSE) :
internal error -3 in R_decompress1
Error in .deparseOpts(control) : "anyNA" is not a BUILTIN function
> traceback()
11: .deparseOpts(control)
10: deparse(x[[1L]])
9: mode(expr)
8: match(x, table, nomatch = 0L)
7: mode(expr) %in% c("call", "expression", "(", "function")
6: deparse(call)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch(expr, error = function(e) {
call <- conditionCall(e)
if (!is.null(call)) {
if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("Error in", dcall, ": ")
LONG <- 75L
msg <- conditionMessage(e)
sm <- strsplit(msg, "\n")[[1L]]
w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type =
"w")
if is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
}
else prefix <- "Error : "
msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))
if (!silent && identical(getOption("show.error.messages"),
TRUE)) {
cat(msg, file = stderr())
.Internal(printDeferredWarnings())
}
invisible(structure(msg, class = "try-error", condition = e))
})
1: try(gsub("\\s+<smb: s+="">", " ",
paste(capture.output(print(args(traceback))),
collapse = "")), silent = TRUE)
------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139
On Jan 17, 2014, at 5:37 PM, Steve Lianoglou
<lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote:
The good news is that it's not too onerous to recover from scratch.
Just download the latest R-release installer pkg from CRAN. The
installer will (should) contain the same warning telling you what the
command is to perform a "non-destructive" isntall. For what it's
worth, you simply have to open up a terminal and type in the following
command:
sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg
Then continue with the installation and all will be Feng Shui.
After doing so, launching "R" from the terminal should now open
R-3.0.2 (no need to use RSwitch). Just do the usual biocinstall (ie.
source the biocLite script then re-install the packages you need).
Being at MIT, the bandwidth available to you should make this a quick
process, especially since the packages for the mac do not need to be
compiled for installation.
[[alternative HTML version deleted]]

Hi Katrina,
Sounds like we're almost there ... comments inline:
On Fri, Jan 17, 2014 at 3:12 PM, Kristina M Fontanez <fontanez at="" mit.edu=""> wrote:
> Hi Steve-
>
> Thanks for the help. I deleted the development and corrupted release
versions of R from my computer. Then, I downloaded the release
version. Next, I renamed the release version in my Applications folder
to R_3.0.
Nice one! Good move on your part to have done that and sorry that I
neglected to point that out earlier -- I don't use R.app, so it
slipped my mind.
> Then I downloaded the installer package from att.com<http: att.com="">
for the development version. I opened up a terminal and in my /
directory I typed in sudo pkgutil ?forget
org.r-project.R.x86_64.fw.pkg.
>
> parsons-three-sixty:/ fontanez$ sudo pkgutil --forget
org.r-project.R.x86_64.fw.pkg
> Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'.
>
> Then, I proceeded to install the development version from the R
development installer package. It installed correctly and I was able
to download the development version of DESeq and my other packages.
However, this is where I ran into a problem.
>
> I shut down R and opened up the R_3.0 app from my Applications. It
opened, which was good but it drops a ton of warnings. Anytime I try
to type something (as I?m typing) that ?anyNA? is not a builtin
function error pops up. It looks like my R 3.0 is still corrupted. I
didn?t change anything in /Library/Frameworks - should I have done
that as well, like Dan suggested?
No, do not change anything in /Library/Frameworks/* manually --
RSwitch handles those "delicate" details for you. So, you now have to
download RSwitch and use that to change the version of R that is
currently "live".
So, if you want to use R 3.0.x, you would:
(i) first quit the current R process you are running
(ii) open up RSwitch and select "R 3.0". This does some magic inside
the /LibraryFrameworks/R.framwork/* for you.
(iii) After selecting that, you can then launch your R_3.0.app
If you want to run R-devel you would
(i) Quit current version of R
(ii) Open up RSwitch and select R 3.1
(iii) open up the R.app that the R-devel package installed for you.
That should do the trick -- if not, please post back with an update as
I'm *pretty* sure you don't have to do anything much more involved
than that.
-steve
--
Steve Lianoglou
Computational Biologist
Genentech

Steve-
Thank you for your help with this issue. Your last post solved my
problems with the errors and I now have R 3.0 and R 3.1 installed side
by side on my system.
Im sorry for the late reply as I was away over the weekend.
Thanks again,
Kristina
------------------------------------------------------------------
Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139
On Jan 17, 2014, at 6:58 PM, Steve Lianoglou
<lianoglou.steve@gene.com<mailto:lianoglou.steve@gene.com>> wrote:
Hi Katrina,
Sounds like we're almost there ... comments inline:
On Fri, Jan 17, 2014 at 3:12 PM, Kristina M Fontanez
<fontanez@mit.edu<mailto:fontanez@mit.edu>> wrote:
Hi Steve-
Thanks for the help. I deleted the development and corrupted release
versions of R from my computer. Then, I downloaded the release
version. Next, I renamed the release version in my Applications folder
to R_3.0.
Nice one! Good move on your part to have done that and sorry that I
neglected to point that out earlier -- I don't use R.app, so it
slipped my mind.
Then I downloaded the installer package from
att.com<http: att.com=""><http: att.com=""> for the development version. I
opened up a terminal and in my / directory I typed in sudo pkgutil
forget org.r-project.R.x86_64.fw.pkg.
parsons-three-sixty:/ fontanez$ sudo pkgutil --forget
org.r-project.R.x86_64.fw.pkg
Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'.
Then, I proceeded to install the development version from the R
development installer package. It installed correctly and I was able
to download the development version of DESeq and my other packages.
However, this is where I ran into a problem.
I shut down R and opened up the R_3.0 app from my Applications. It
opened, which was good but it drops a ton of warnings. Anytime I try
to type something (as Im typing) that anyNA is not a builtin
function error pops up. It looks like my R 3.0 is still corrupted. I
didnt change anything in /Library/Frameworks - should I have done
that as well, like Dan suggested?
No, do not change anything in /Library/Frameworks/* manually --
RSwitch handles those "delicate" details for you. So, you now have to
download RSwitch and use that to change the version of R that is
currently "live".
So, if you want to use R 3.0.x, you would:
(i) first quit the current R process you are running
(ii) open up RSwitch and select "R 3.0". This does some magic inside
the /LibraryFrameworks/R.framwork/* for you.
(iii) After selecting that, you can then launch your R_3.0.app
If you want to run R-devel you would
(i) Quit current version of R
(ii) Open up RSwitch and select R 3.1
(iii) open up the R.app that the R-devel package installed for you.
That should do the trick -- if not, please post back with an update as
I'm *pretty* sure you don't have to do anything much more involved
than that.
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
[[alternative HTML version deleted]]